The Church was built in 1229 on the spot where the Saint had preached and carried out a miracle in 1212. There is a fresco inside the church depicting this miracle in which the Saint uses a duck to free a child savaged by a wolf. This fresco has been recently restored to its original state. During restoration work in or around the seventeenth century, the fresco had been repainted in a different colour using casein tempera that not only changed the colour of some of the components in the painting but also resulted in the addition of a landscape scene in the background, thus reflecting the artistic taste of that period. Following several tests to remove the retouched part using the "buon fresco" technique there appeared an entire fresco dating back to the fourteenth century showing a simplified scene with Giottesque particulars and tenets. A rare fresco depicting the chief Franciscan martyrs can be seen inside the convent.

The Convent flourished during the seventeenth century. Blessed Gonella da Norcia died here on 22 June 1540. In 1608 the fine cloister was built and embellished with a series of elegant columns in travertine stone and frescoes showing the life of Saint Francesco. The belfry tending towards the baroque style was built in 1680 and can still be admired today. Until 1930 the convent was a flourishing religious centre. In 1988, the Saint Francesco Association ("Associazione san Francesco") had the church roof redone, this work was followed by the removal of the granolithic floor put down in 1950, thus enabling the old terracotta brick floor to return to its former splendour. In 2004, a beautiful altar was built and the old walnut entrance door to the church was restored in memory of Mario Tessicini, the first President of the Saint Francesco Association.